Linking Nucleotides
Home Up Nucleotide Structure Nucleotide Variations Linking Nucleotides RNA Structure DNA Structure

 

Linking Nucleotides

On this page we will look at how the nucleotides (the ones with one phosphate group) bond to one another to form nucleic acids.

For reasons that will soon become obvious, I'm going to make several changes in the way that I have represented the structure here. (One is to add that oxygen that I had inadvertently left out before.) Another is to rotate the phosphate. Also, instead of writing out the structure of the base, I will just write "base" and change the angle a little bit.

Again, keep in mind that this is a two-dimensional drawing, so it really doesn't represent the actual shape of this molecule.

Structure of nucleotide. [69024.jpg]
Altered structure of nucleotide. [69025.jpg]

 

The nucleotides bond to one another in a sequence of catalyzed dehydration reactions. One OH group on the phosphate and the OH group on the third carbon of the sugar are the functional groups which allow for the polymerization of the nucleotides into a polynucleotide or nucleic acid.

Structure of two nucleotides linked together. [69026.jpg]
Note that the phosphate group links the third carbon of one sugar molecule to the fifth carbon of the next sugar molecule. Because of that, this can be called a 3'-5' phosphate ester link (or a 3'-5' phospho diester link, pronounced 3-prime, 5-prime (3'-5') phospho diester). The carbon atoms in the ribose portion of a nucleotide are numbered with primes (1', 2', 3', 4', 5') to distinguish them from the carbon and nitrogen atoms in the base which are numbered without primes.

Structure of three nucteotides linked together. [69027.jpg]

 

You may have wondered (as I did when I first learned about DNA and RNA) why these chemicals are called nucleic acids if they are made up of bases. Well, it's the hydrogen that still remains on the phosphate group from the phosphoric acid that is acidic and gives these nucleic acids their acidic nature and thus, their name, nucleic acids. Because these hydrogens are acidic, they can come off and when they do so, they would leave behind a negative charge on the nucleic acid molecule. (At that point you actually have the conjugate base of the nucleic acid.) Depending on the references that you work with, you may see these molecules written with the hydrogens on (as shown above) or with the hydrogens removed and a negative sign in their place. Undoubtably, at biological pH, an equilibriium exists and both forms are present.

 

Top of Page

E-mail instructor: Sue Eggling

Clackamas Community College
©2001, 2003 Clackamas Community College, Hal Bender